Do you use the Kindle app as well?
Can you make annotations in your reading using the S-Pen?

Do I use Kindle app? Yes I do! In fact recently I've been using the Kindle app on my Note much more often than hardware Kindle.

As for annotations - Kindle app for Android is still quite limited, so I cannot draw over the page, underline words etc. I can, however, select words and make standard Kindle notes (text, not graphics).

As for rooting your Note, the Zergrush method is rather foolproof and there are ready packages, so as long as you follow the procedure, there is very little risk. The newest firmwares, however, aren't directly rootable, so you need to downgrade first, root and then upgrade the firmware again (through Odin or Mobile Odin, keeping the root).